The intestinal microbiota represent the largest mass and diversity of antigens encountered by the host immune system. Exposure to the microbiota is known to have profound effects on the mucosal immune system, which develop largely in response to microbial stimulation. The effects on the systemic immune system are less clear, but there are increasing data indicating that exposure to the microbes in the intestine can alter the development of immune diseases later in life. For example, provision of probiotic bacteria to newborn infants who had a high susceptibility to atopy reduced the incidence of this condition by 50% by age 5. One explanation of such data is that exposure to the microbiota, and possibly intestinal pathogens, early in life defines patterns of immune reactivity that can result in inflammatory or autoimmune diseases as individuals age.
The host immune response to the microbiota continues throughout life. This likely explains why the majority of lymphocytes and immunoglobulins in the body are located in the intestine. Some 3-5 gm of IgA are produced daily in the normal human intestine. There appears to be active communication among the microbiota, the intestinal epithelium, and the immune system. The innate immune system plays a particularly important role in the host response to the microbiota and, in turn, is sustained by this exposure. Adaptive immune responses to antigens of the microbiota in mice are compartmented tightly to the intestine and consist mainly of IgA in the secretions. Recent data indicate that there is no serum IgG antibody or systemic T cell reactivity to microbiota antigens detectable in normal mice; however, detectable levels of serum IgG antibody and systemic T cell reactivity were present in mice with colitis. The human response to the microbiota is largely undefined, but there do appear to be serum IgG antibodies to microbial antigens in normal humans. What those antigens are is yet to be defined.
A set of immunodominant microbiota antigens from mice has been cloned. These were defined using serum from colitic mice to screen a DNA library derived from murine commensal bacteria. These recombinant proteins represent a small fraction of the total potential proteins of the microbiota. Among these antigens, commensal bacterial flagellins represented some 20-25% of the total, which is entirely disproportionate to their representation in the total antigen pool. In addition, half of the subjects with Crohn's disease were found to have IgG antibodies to certain flagellin molecules, a reactivity that was not detected in normal humans or in subjects with a related inflammatory bowel disease, ulcerative colitis. Subsequent studies have found that Crohn's subjects with IgG antibodies to certain flagellin antigens have a more refractory or complicated course, illustrating that this seroreactivity is reflecting a pattern of host immune reactivity. Thus, IgG antibodies to these flagellin proteins of the microbiota can represent a biologic marker of prognostic value in Crohn's disease.
Crohn's Disease and ulcerative colitis (collectively referred to as inflammatory bowel disease, or IBD) are chronic, inflammatory diseases of the gastrointestinal tract. While the clinical features vary somewhat between these two disorders, both are characterized by abdominal pain, diarrhea (often bloody), a variable group of extra-intestinal manifestations (such as arthritis, uveitis, skin changes, etc.) and the accumulation of inflammatory cells within the small intestine and colon (observed in pathologic biopsy or surgical specimens).
IBD affects both children and adults, and has a bimodal age distribution (one peak around 20, and a second around 40). IBD is a chronic, lifelong disease, and is often grouped with other so-called “autoimmune” disorders (e.g. rheumatoid arthritis, type I diabetes mellitus, multiple sclerosis, etc.). IBD is found almost exclusively in the industrialized world. The most recent data from the Mayo Clinic suggest an overall incidence greater than 1 in 100,000 people in the United States, with prevalence data in some studies greater than 1 in 1000. There is a clear trend towards the increasing incidence of IBD in the US and Europe, particularly Crohn's Disease. The basis for this increase is not presently clear. As such, IBD represents the 2.sup.nd most common autoimmune disease in the United States (after rheumatoid arthritis).
Treatment of IBD is varied. First line therapy typically includes salicylate derivatives (e.g., 5-ASA) given orally or rectally. Response rates in uncomplicated Crohn's Disease are approximately 40% (compared to 20% for placebo). Corticosteroids remain a mainstay in the treatment of subjects with more “refractory” disease, despite the side-effects. Newer treatment options include anti-metabolites (e.g., methotrexate, 6-mercaptopurine) and immunomodulators (e.g. Remicade—a chimeric human antibody directed at the TNFα receptor).
There are many parallels between IBD and other immune-mediated inflammatory diseases (collectively known as IMIDs). IMIDs also affect both children and adults. As with IBD, treatments of IMIDs are varied but unsatisfactory because they do not change the natural history of these diseases. In spite of considerable research into therapies for these disorders, IMIDs remain difficult to diagnose and treat effectively. Furthermore, there are few laboratory tests that are diagnostic for IMIDS, and suitable laboratory tests that serve as “surrogate marker” that are uniformly useful to follow the course of disease in subjects are lacking. Accordingly, there is a need in the art for improved methods of detecting and treating such inflammatory bowel diseases. The present invention fulfills these needs and further provides other related advantages.
The properties that make a protein antigenic in one species are general and likely to be shared among other species. Thus, immunodominant antigens in mice will also be immunodominant in humans. Autoantigens are highly conserved among species and are not restricted to a given species. The same is true for antigens of the microbiota. Thus, the use of antigens of microbiota are widely useful.
Furthermore, because the microbiota represent the greatest mass of foreign antigen that the body encounters, the host immune response to the microbiota influences or determines immune reactivity to other antigens, including autoantigens. At a minimum, reactivity to the microbiota reflects the pattern of an individual's host immune reactivity.
Measurement of antibody reactivity to a panel or array of immunodominant antigens of the microbial flora reveals patterns of host immune reactivity that determine susceptibility to or severity of immune-mediated inflammatory and autoimmune diseases. Antibodies to the microbiota serve as a register and archive of the host antigenic experience with this large mass of microbial environmental antigens, both past and present. These antibody biomarkers provide a window into the immune system that was not previously available. These antigens and polynucleotides that encode them provide novel therapies because: alteration of the immune response to these microbiota antigens modulate immune reactivity to other antigens that drive the disease process.